@saibolla/ada 0.1.2

package/skills/scientific-slides/references/beamer_guide.md

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+# LaTeX Beamer Guide for Scientific Presentations
+
+## Overview
+
+Beamer is a LaTeX document class for creating presentations with professional, consistent formatting. It's particularly well-suited for scientific presentations containing equations, code, algorithms, and citations. This guide covers Beamer basics, themes, customization, and advanced features for effective scientific talks.
+
+## Why Use Beamer?
+
+### Advantages
+
+**Professional Quality**:
+- Consistent, polished appearance
+- Beautiful typography (especially for math)
+- Publication-quality output
+- Professional themes and templates
+
+**Scientific Content**:
+- Native equation support (LaTeX math)
+- Code listings with syntax highlighting
+- Algorithm environments
+- Bibliography integration
+- Cross-referencing
+
+**Reproducibility**:
+- Plain text source (version control friendly)
+- Programmatic figure generation
+- Consistent styling across presentations
+- Easy to maintain and update
+
+**Efficiency**:
+- Reuse content across presentations
+- Template once, use forever
+- Automated elements (page numbers, navigation)
+- No manual formatting
+
+### Disadvantages
+
+**Learning Curve**:
+- Requires LaTeX knowledge
+- Compilation time
+- Debugging can be challenging
+- Less WYSIWYG than PowerPoint
+
+**Flexibility**:
+- Complex custom layouts require effort
+- Image editing requires external tools
+- Some design elements easier in PowerPoint
+- Animations more limited
+
+**Collaboration**:
+- Not ideal for non-LaTeX users
+- Version conflicts possible
+- Requires LaTeX installation
+
+## Basic Beamer Document Structure
+
+### Minimal Example
+
+```latex
+\documentclass{beamer}
+
+% Theme
+\usetheme{Madrid}
+\usecolortheme{beaver}
+
+% Title information
+\title{Your Presentation Title}
+\subtitle{Optional Subtitle}
+\author{Your Name}
+\institute{Your Institution}
+\date{\today}
+
+\begin{document}
+
+% Title slide
+\begin{frame}
+  \titlepage
+\end{frame}
+
+% Content slide
+\begin{frame}{Slide Title}
+  Content goes here
+\end{frame}
+
+\end{document}
+```
+
+### Essential Packages
+
+```latex
+\documentclass{beamer}
+
+% Encoding and fonts
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+
+% Graphics
+\usepackage{graphicx}
+\graphicspath{{./figures/}}
+
+% Math
+\usepackage{amsmath, amssymb, amsthm}
+
+% Tables
+\usepackage{booktabs}
+\usepackage{multirow}
+
+% Colors
+\usepackage{xcolor}
+
+% Algorithms
+\usepackage{algorithm}
+\usepackage{algorithmic}
+
+% Code listings
+\usepackage{listings}
+
+% Citations
+\usepackage[style=authoryear,backend=biber]{biblatex}
+\addbibresource{references.bib}
+```
+
+### Frame Basics
+
+```latex
+% Basic frame
+\begin{frame}{Title}
+  Content
+\end{frame}
+
+% Frame with subtitle
+\begin{frame}{Title}{Subtitle}
+  Content
+\end{frame}
+
+% Frame without title
+\begin{frame}
+  Content
+\end{frame}
+
+% Fragile frame (for verbatim/code)
+\begin{frame}[fragile]{Code Example}
+  \begin{verbatim}
+  def hello():
+      print("Hello")
+  \end{verbatim}
+\end{frame}
+
+% Plain frame (no header/footer)
+\begin{frame}[plain]
+  Full slide content
+\end{frame}
+```
+
+## Themes and Appearance
+
+### Presentation Themes
+
+Beamer includes many built-in themes controlling overall layout:
+
+**Classic Themes**:
+```latex
+\usetheme{Berlin}      % Sections in header
+\usetheme{Copenhagen}  % Minimal, clean
+\usetheme{Madrid}      % Professional, rounded
+\usetheme{Boadilla}    % Simple footer
+\usetheme{AnnArbor}    % Vertical navigation
+```
+
+**Modern Themes**:
+```latex
+\usetheme{CambridgeUS}  % Blue theme
+\usetheme{Singapore}    % Minimalist
+\usetheme{Rochester}    % Very minimal
+\usetheme{Antibes}      % Tree navigation
+```
+
+**Popular for Science**:
+```latex
+% Clean and minimal
+\usetheme{default}
+\usetheme{Copenhagen}
+
+% Professional with navigation
+\usetheme{Madrid}
+\usetheme{Berlin}
+
+% Traditional academic
+\usetheme{Pittsburgh}
+\usetheme{Boadilla}
+```
+
+### Color Themes
+
+```latex
+% Blue themes
+\usecolortheme{default}      % Blue
+\usecolortheme{dolphin}      % Cyan-blue
+\usecolortheme{seagull}      % Grayscale
+
+% Warm themes
+\usecolortheme{beaver}       % Red/brown
+\usecolortheme{rose}         % Pink/red
+
+% Nature themes
+\usecolortheme{orchid}       % Purple
+\usecolortheme{crane}        % Orange/yellow
+
+% Professional
+\usecolortheme{albatross}    % Gray/blue
+```
+
+### Font Themes
+
+```latex
+\usefonttheme{default}              % Standard
+\usefonttheme{serif}                % Serif fonts
+\usefonttheme{structurebold}        % Bold structure
+\usefonttheme{structureitalicserif} % Italic serif
+\usefonttheme{professionalfonts}    % Professional fonts
+```
+
+### Custom Colors
+
+```latex
+% Define custom colors
+\definecolor{myblue}{RGB}{0,115,178}
+\definecolor{myred}{RGB}{214,40,40}
+
+% Apply to theme elements
+\setbeamercolor{structure}{fg=myblue}
+\setbeamercolor{title}{fg=myred}
+\setbeamercolor{frametitle}{fg=myblue,bg=white}
+\setbeamercolor{block title}{fg=white,bg=myblue}
+```
+
+### Minimal Custom Theme
+
+```latex
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Page numbers
+\setbeamertemplate{footline}[frame number]
+
+% Simple itemize
+\setbeamertemplate{itemize items}[circle]
+
+% Clean blocks
+\setbeamertemplate{blocks}[rounded][shadow=false]
+
+% Colors
+\setbeamercolor{structure}{fg=blue!70!black}
+\setbeamercolor{title}{fg=black}
+\setbeamercolor{frametitle}{fg=blue!70!black}
+```
+
+## Content Elements
+
+### Lists
+
+**Itemize**:
+```latex
+\begin{frame}{Bullet Points}
+  \begin{itemize}
+    \item First point
+    \item Second point
+      \begin{itemize}
+        \item Nested point
+      \end{itemize}
+    \item Third point
+  \end{itemize}
+\end{frame}
+```
+
+**Enumerate**:
+```latex
+\begin{frame}{Numbered List}
+  \begin{enumerate}
+    \item First item
+    \item Second item
+    \item Third item
+  \end{enumerate}
+\end{frame}
+```
+
+**Description**:
+```latex
+\begin{frame}{Definitions}
+  \begin{description}
+    \item[Term 1] Definition of term 1
+    \item[Term 2] Definition of term 2
+  \end{description}
+\end{frame}
+```
+
+### Columns
+
+```latex
+\begin{frame}{Two Column Layout}
+  \begin{columns}
+    
+    % Left column
+    \begin{column}{0.5\textwidth}
+      \begin{itemize}
+        \item Point 1
+        \item Point 2
+      \end{itemize}
+    \end{column}
+    
+    % Right column
+    \begin{column}{0.5\textwidth}
+      \includegraphics[width=\textwidth]{figure.png}
+    \end{column}
+    
+  \end{columns}
+\end{frame}
+```
+
+**Three Column Layout**:
+```latex
+\begin{columns}[T] % Align at top
+  \begin{column}{0.32\textwidth}
+    Content A
+  \end{column}
+  \begin{column}{0.32\textwidth}
+    Content B
+  \end{column}
+  \begin{column}{0.32\textwidth}
+    Content C
+  \end{column}
+\end{columns}
+```
+
+### Figures
+
+```latex
+\begin{frame}{Figure Example}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.8\textwidth]{figure.pdf}
+    \caption{Figure caption text}
+  \end{figure}
+\end{frame}
+```
+
+**Side-by-Side Figures**:
+```latex
+\begin{frame}{Comparison}
+  \begin{columns}
+    \begin{column}{0.5\textwidth}
+      \includegraphics[width=\textwidth]{fig1.pdf}
+      \caption{Condition A}
+    \end{column}
+    \begin{column}{0.5\textwidth}
+      \includegraphics[width=\textwidth]{fig2.pdf}
+      \caption{Condition B}
+    \end{column}
+  \end{columns}
+\end{frame}
+```
+
+**Subfigures**:
+```latex
+\usepackage{subcaption}
+
+\begin{frame}{Multiple Panels}
+  \begin{figure}
+    \centering
+    \begin{subfigure}{0.45\textwidth}
+      \includegraphics[width=\textwidth]{fig1.pdf}
+      \caption{Panel A}
+    \end{subfigure}
+    \hfill
+    \begin{subfigure}{0.45\textwidth}
+      \includegraphics[width=\textwidth]{fig2.pdf}
+      \caption{Panel B}
+    \end{subfigure}
+    \caption{Overall figure caption}
+  \end{figure}
+\end{frame}
+```
+
+### Tables
+
+```latex
+\begin{frame}{Table Example}
+  \begin{table}
+    \centering
+    \begin{tabular}{lcc}
+      \toprule
+      Method & Accuracy & Time \\
+      \midrule
+      Method A & 0.85 & 10s \\
+      Method B & 0.92 & 25s \\
+      Method C & 0.88 & 15s \\
+      \bottomrule
+    \end{tabular}
+    \caption{Performance comparison}
+  \end{table}
+\end{frame}
+```
+
+### Blocks
+
+**Standard Blocks**:
+```latex
+\begin{frame}{Block Examples}
+  
+  % Standard block
+  \begin{block}{Block Title}
+    Block content goes here
+  \end{block}
+  
+  % Alert block (red)
+  \begin{alertblock}{Important}
+    Warning or important information
+  \end{alertblock}
+  
+  % Example block (green)
+  \begin{exampleblock}{Example}
+    Example content
+  \end{exampleblock}
+  
+\end{frame}
+```
+
+**Theorem Environments**:
+```latex
+\begin{frame}{Mathematical Results}
+  
+  \begin{theorem}
+    Statement of theorem
+  \end{theorem}
+  
+  \begin{proof}
+    Proof goes here
+  \end{proof}
+  
+  \begin{definition}
+    Definition text
+  \end{definition}
+  
+  \begin{lemma}
+    Lemma statement
+  \end{lemma}
+  
+\end{frame}
+```
+
+## Overlays and Animations
+
+### Progressive Disclosure with \pause
+
+```latex
+\begin{frame}{Revealing Content}
+  First point appears immediately
+  
+  \pause
+  
+  Second point appears on click
+  
+  \pause
+  
+  Third point appears on another click
+\end{frame}
+```
+
+### Overlay Specifications
+
+**Itemize with Overlays**:
+```latex
+\begin{frame}{Sequential Bullets}
+  \begin{itemize}
+    \item<1-> Appears on slide 1 and stays
+    \item<2-> Appears on slide 2 and stays
+    \item<3-> Appears on slide 3 and stays
+  \end{itemize}
+\end{frame}
+```
+
+**Alternative Syntax**:
+```latex
+\begin{frame}{Sequential Bullets}
+  \begin{itemize}[<+->]  % Automatically sequential
+    \item First point
+    \item Second point
+    \item Third point
+  \end{itemize}
+\end{frame}
+```
+
+### Highlighting with Overlays
+
+**Alert on Specific Slides**:
+```latex
+\begin{frame}{Highlighting}
+  \begin{itemize}
+    \item Normal text
+    \item<2-| alert@2> Text highlighted on slide 2
+    \item Normal text
+  \end{itemize}
+\end{frame}
+```
+
+**Temporary Appearance**:
+```latex
+\begin{frame}{Appearing and Disappearing}
+  Appears on all slides
+  
+  \only<2>{Only visible on slide 2}
+  
+  \uncover<3->{Appears on slide 3 and stays}
+  
+  \visible<4->{Also appears on slide 4, but reserves space}
+\end{frame}
+```
+
+### Building Complex Figures
+
+```latex
+\begin{frame}{Building a Figure}
+  \begin{tikzpicture}
+    % Base elements (always visible)
+    \draw (0,0) rectangle (4,3);
+    
+    % Add on slide 2+
+    \draw<2-> (1,1) circle (0.5);
+    
+    % Add on slide 3+
+    \draw<3->[->, thick] (2,1.5) -- (3,2);
+    
+    % Highlight on slide 4
+    \node<4>[red,thick] at (2,1.5) {Result};
+  \end{tikzpicture}
+\end{frame}
+```
+
+## Mathematical Content
+
+### Equations
+
+**Inline Math**:
+```latex
+\begin{frame}{Inline Math}
+  The equation $E = mc^2$ is famous.
+  
+  We can also write $\alpha + \beta = \gamma$.
+\end{frame}
+```
+
+**Display Math**:
+```latex
+\begin{frame}{Display Equations}
+  Single equation:
+  \begin{equation}
+    f(x) = \int_{-\infty}^{\infty} e^{-x^2} dx = \sqrt{\pi}
+  \end{equation}
+  
+  Multiple equations:
+  \begin{align}
+    E &= mc^2 \\
+    F &= ma \\
+    V &= IR
+  \end{align}
+\end{frame}
+```
+
+**Equation Arrays**:
+```latex
+\begin{frame}{Equation System}
+  \begin{equation}
+    \begin{cases}
+      \dot{x} = f(x,y) \\
+      \dot{y} = g(x,y)
+    \end{cases}
+  \end{equation}
+\end{frame}
+```
+
+### Matrices
+
+```latex
+\begin{frame}{Matrix Example}
+  \begin{equation}
+    A = \begin{bmatrix}
+      a_{11} & a_{12} & a_{13} \\
+      a_{21} & a_{22} & a_{23} \\
+      a_{31} & a_{32} & a_{33}
+    \end{bmatrix}
+  \end{equation}
+\end{frame}
+```
+
+## Code and Algorithms
+
+### Code Listings
+
+```latex
+\begin{frame}[fragile]{Python Code}
+  \begin{lstlisting}[language=Python]
+def fibonacci(n):
+    if n <= 1:
+        return n
+    return fibonacci(n-1) + fibonacci(n-2)
+  \end{lstlisting}
+\end{frame}
+```
+
+**Custom Code Styling**:
+```latex
+\lstset{
+  language=Python,
+  basicstyle=\ttfamily\small,
+  keywordstyle=\color{blue},
+  commentstyle=\color{green!60!black},
+  stringstyle=\color{orange},
+  numbers=left,
+  numberstyle=\tiny,
+  frame=single,
+  breaklines=true
+}
+
+\begin{frame}[fragile]{Styled Code}
+  \begin{lstlisting}
+  # This is a comment
+  def hello(name):
+      """Greet someone"""
+      print(f"Hello, {name}")
+  \end{lstlisting}
+\end{frame}
+```
+
+### Algorithms
+
+```latex
+\begin{frame}{Algorithm Example}
+  \begin{algorithm}[H]
+    \caption{Quicksort}
+    \begin{algorithmic}[1]
+      \REQUIRE Array $A$, indices $low$, $high$
+      \ENSURE Sorted array
+      \IF{$low < high$}
+        \STATE $pivot \gets partition(A, low, high)$
+        \STATE $quicksort(A, low, pivot-1)$
+        \STATE $quicksort(A, pivot+1, high)$
+      \ENDIF
+    \end{algorithmic}
+  \end{algorithm}
+\end{frame}
+```
+
+## Citations and Bibliography
+
+### Inline Citations
+
+```latex
+\begin{frame}{Background}
+  Previous work \cite{smith2020} showed that...
+  
+  Multiple studies \cite{jones2019,brown2021} have found...
+  
+  According to \textcite{davis2022}, the method works by...
+\end{frame}
+```
+
+### Bibliography Slide
+
+```latex
+% At end of presentation
+\begin{frame}[allowframebreaks]{References}
+  \printbibliography
+\end{frame}
+```
+
+### Custom Bibliography Style
+
+```latex
+% In preamble
+\usepackage[style=authoryear,maxbibnames=2,maxcitenames=2]{biblatex}
+\addbibresource{references.bib}
+
+% Smaller font for references
+\renewcommand*{\bibfont}{\scriptsize}
+```
+
+## Advanced Features
+
+### Section Organization
+
+```latex
+\section{Introduction}
+\begin{frame}{Introduction}
+  Content
+\end{frame}
+
+\section{Methods}
+\begin{frame}{Methods}
+  Content
+\end{frame}
+
+% Automatic outline
+\begin{frame}{Outline}
+  \tableofcontents
+\end{frame}
+
+% Outline at each section
+\AtBeginSection{
+  \begin{frame}{Outline}
+    \tableofcontents[currentsection]
+  \end{frame}
+}
+```
+
+### Backup Slides
+
+```latex
+% Main presentation ends
+\begin{frame}{Thank You}
+  Questions?
+\end{frame}
+
+% Backup slides (not counted in numbering)
+\appendix
+
+\begin{frame}{Extra Data}
+  Additional analysis for questions
+\end{frame}
+
+\begin{frame}{Detailed Methods}
+  More methodological details
+\end{frame}
+```
+
+### Hyperlinks
+
+```latex
+% Define labels
+\begin{frame}{Main Result}
+  \label{mainresult}
+  This is the main finding.
+\end{frame}
+
+% Link to labeled frame
+\begin{frame}{Reference}
+  As shown in the \hyperlink{mainresult}{main result}...
+\end{frame}
+
+% External links
+\begin{frame}{Resources}
+  Visit \url{https://example.com} for more information.
+  
+  \href{https://github.com/user/repo}{GitHub Repository}
+\end{frame}
+```
+
+### QR Codes
+
+```latex
+\usepackage{qrcode}
+
+\begin{frame}{Scan for Paper}
+  \begin{center}
+    \qrcode[height=3cm]{https://doi.org/10.1234/paper}
+    
+    \vspace{0.5cm}
+    Scan for full paper
+  \end{center}
+\end{frame}
+```
+
+### Multimedia
+
+```latex
+\usepackage{multimedia}
+
+\begin{frame}{Video}
+  \movie[width=8cm,height=6cm]{Click to play}{video.mp4}
+\end{frame}
+```
+
+**Note**: Multimedia support varies by PDF viewer.
+
+## TikZ Graphics
+
+### Basic Shapes
+
+```latex
+\usepackage{tikz}
+
+\begin{frame}{TikZ Example}
+  \begin{tikzpicture}
+    % Rectangle
+    \draw (0,0) rectangle (2,1);
+    
+    % Circle
+    \draw (3,0.5) circle (0.5);
+    
+    % Line with arrow
+    \draw[->, thick] (0,0) -- (3,2);
+    
+    % Node with text
+    \node at (1.5,2) {Label};
+  \end{tikzpicture}
+\end{frame}
+```
+
+### Flowcharts
+
+```latex
+\usetikzlibrary{shapes,arrows,positioning}
+
+\begin{frame}{Workflow}
+  \begin{tikzpicture}[node distance=2cm]
+    \node[rectangle,draw] (start) {Start};
+    \node[rectangle,draw,right=of start] (process) {Process};
+    \node[rectangle,draw,right=of process] (end) {End};
+    
+    \draw[->,thick] (start) -- (process);
+    \draw[->,thick] (process) -- (end);
+  \end{tikzpicture}
+\end{frame}
+```
+
+### Plots
+
+```latex
+\usepackage{pgfplots}
+\pgfplotsset{compat=1.18}
+
+\begin{frame}{Data Plot}
+  \begin{tikzpicture}
+    \begin{axis}[
+      xlabel={$x$},
+      ylabel={$y$},
+      width=8cm,
+      height=6cm
+    ]
+    \addplot[blue,thick] coordinates {
+      (0,0) (1,1) (2,4) (3,9)
+    };
+    \addplot[red,dashed] {x};
+    \end{axis}
+  \end{tikzpicture}
+\end{frame}
+```
+
+## Compilation
+
+### Basic Compilation
+
+```bash
+# Standard compilation
+pdflatex presentation.tex
+
+# With bibliography
+pdflatex presentation.tex
+biber presentation
+pdflatex presentation.tex
+pdflatex presentation.tex
+```
+
+### Modern Compilation (Recommended)
+
+```bash
+# Using latexmk (automated)
+latexmk -pdf presentation.tex
+
+# With continuous preview
+latexmk -pdf -pvc presentation.tex
+```
+
+### Compilation Options
+
+```bash
+# Faster compilation (draft mode)
+pdflatex -draftmode presentation.tex
+
+# Specific engine
+lualatex presentation.tex    # Better Unicode support
+xelatex presentation.tex     # System fonts
+
+# Output directory
+pdflatex -output-directory=build presentation.tex
+```
+
+## Handouts and Notes
+
+### Creating Handouts
+
+```latex
+% In preamble
+\documentclass[handout]{beamer}
+
+% This removes overlays and creates one frame per slide
+```
+
+### Speaker Notes
+
+```latex
+\usepackage{pgfpages}
+\setbeameroption{show notes on second screen=right}
+
+\begin{frame}{Slide Title}
+  Slide content visible to audience
+  
+  \note{
+    These notes are visible only to speaker:
+    - Remember to emphasize X
+    - Mention collaboration with Y
+    - Expect question about Z
+  }
+\end{frame}
+```
+
+### Handout with Notes
+
+```latex
+\documentclass[handout]{beamer}
+\usepackage{pgfpages}
+\pgfpagesuselayout{2 on 1}[a4paper,border shrink=5mm]
+```
+
+## Best Practices
+
+### Do's
+
+- ✅ Use consistent theme throughout
+- ✅ Keep equations simple and large
+- ✅ Use progressive disclosure (\pause, overlays)
+- ✅ Include frame numbers
+- ✅ Use vector graphics (PDF) for figures
+- ✅ Test compilation early and often
+- ✅ Use meaningful section names
+- ✅ Keep backup slides in appendix
+
+### Don'ts
+
+- ❌ Don't use too many different fonts or colors
+- ❌ Don't fill slides with dense text
+- ❌ Don't use tiny font sizes
+- ❌ Don't include complex animations (limited support)
+- ❌ Don't forget fragile frames for code
+- ❌ Don't mix themes inconsistently
+- ❌ Don't ignore compilation warnings
+
+## Troubleshooting
+
+### Common Issues
+
+**Missing Fragile**:
+```
+Error: Verbatim environment in frame
+Solution: Add [fragile] option to frame
+```
+
+**Package Conflicts**:
+```
+Error: Option clash for package X
+Solution: Load package in preamble only once
+```
+
+**Image Not Found**:
+```
+Error: File `figure.pdf' not found
+Solution: Check path, use \graphicspath, ensure file exists
+```
+
+**Overlay Issues**:
+```
+Problem: Overlays not working as expected
+Solution: Check syntax <n-> vs <n-m>, test incremental builds
+```
+
+### Debugging Tips
+
+```latex
+% Show frame labels
+\usepackage[notref,notcite]{showkeys}
+
+% Draft mode (faster, shows boxes)
+\documentclass[draft]{beamer}
+
+% Verbose error messages
+\errorcontextlines=999
+```
+
+## Templates and Examples
+
+### Minimal Working Example
+
+See `assets/beamer_template_conference.tex` for a complete, customizable template for conference talks.
+
+### Resources
+
+- Beamer User Guide: `texdoc beamer`
+- Theme Gallery: https://deic.uab.cat/~iblanes/beamer_gallery/
+- TikZ Examples: https://texample.net/tikz/
+
+## Summary
+
+Beamer excels at:
+- Mathematical content
+- Consistent professional formatting
+- Reproducible presentations
+- Version control
+- Citations and cross-references
+
+Choose Beamer when:
+- Presentation contains significant math/equations
+- You value version control and plain text
+- Consistent styling is priority
+- You're comfortable with LaTeX
+
+Consider PowerPoint when:
+- Extensive custom graphics needed
+- Collaborating with non-LaTeX users
+- Complex animations required
+- Rapid prototyping needed